Abstract

Background

Phylogenies capture the evolutionary ancestry linking extant species. Correlations
and similarities among a set of species are mediated by and need to be understood
in terms of the phylogenic tree. In a similar way it has been argued that biological
networks also induce correlations among sets of interacting genes or their protein
products.

Results

We develop suitable statistical resampling schemes that can incorporate these two
potential sources of correlation into a single inferential framework. To illustrate
our approach we apply it to protein interaction data in yeast and investigate whether
the phylogenetic trees of interacting proteins in a panel of yeast species are more
similar than would be expected by chance.

Conclusions

While we find only negligible evidence for such increased levels of similarities,
our statistical approach allows us to resolve the previously reported contradictory
results on the levels of co-evolution induced by protein-protein interactions. We
conclude with a discussion as to how we may employ the statistical framework developed
here in further functional and evolutionary analyses of biological networks and systems.